The present building, which was completed from 1739-1740, has been designated by the Holy See as the "Mother and Head of all Churches in the Philippines" (Mater et Caput... Omnium Ecclesiarum Insularum Philippinarum).[4]

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The church of the Holy Child was founded by Fray Andrés de Urdaneta, O.S.A. on April 28, 1565, the day when the image of the Holy Child was found in a partially burned hut. More than a week passed after the rediscovery of the image of Santo Niño, on May 8, 1565, Miguel Lopez de Legazpi initiated the founding of the first Spanish settlement in the Philippines. On the spot of the house where the image of the Santo Niño was found, the monastery of the Holy Name of Jesus was constructed. The image was therefore brought to its new shrine in a solemn procession.

The first church believed to be built on the site where the image of the Holy Child was found was burned down in November 1, 1566. It was said to be built by Fr. Diego de Herrera using wood and nipa. Fray Pedro Torres, O.S.A. started the construction of a new church in 1605. It was finished in 1626 but was again burned on March 1628. Fray Juan Medina, O.S.A.[5] started the construction of another church in 1628, using stone and bricks, a great innovation at that time. The construction was stopped because the structure was found to be defective.

On February 29, 1735, Father Provincial Bergaño, Governor-General Fernando Valdes, Bishop Manuel Antonio Decio y Ocampo of Cebu and Fray Juan de Albarran, O.S.A. started the foundations of the present church, using stone. Since the friars did not have the means to complete the church, they enlisted the help of the parishioners of Opon and San Nicolas to contribute materials, while the people of Talisay contributed labor. The lack of chief craftsmen and officers forced Fray Albarran to acquire some knowledge of architecture.[2]

The church was finished not later than 1739.

On January 16, 1740, the miraculous image was enthroned in the new Augustinian church.

In 1789, the church underwent a renovation. On 1889, Fray Mateo Diez, O.S.A. did another renovation. The original features of the church have been retained except for the windows which he added.

In 1960’s, both church and convent underwent a bigger restoration on the occasion of the Fourth Centennial of the Christianization of the country. The face lifting was made with utmost respect for the historical character of the old structure.

In 1965, His Eminence Ildebrando Cardinal Antoniutti, Papal Legate to the Philippines, conferred the church the honorific title Basilica Minore upon the authority of Pope Paul VI. As a Basilica Minore, it is given precedence over other churches and other privileges. Philippine President Ferdinand E. Marcos also declared it a National Landmark.

The devotees keep increasing over the years and could easily fill the Basilica. To accommodate this growing number of devotees who come to hear mass in the Basilica, a pilgrim center was built within the church compound opposite of the Basilica and Holy Mass is celebrated on Fridays and other Religious Festivities are held here in the open-air, theater-like structure.

Completed in September 1990, this open-air structure can accommodate 3,500 people. The basement of the Pilgrim's Center houses the Basilica Del Sto. Niño Museum. [1]

On October 15, 2013, at approximately 8am GMT+8, a 7.2-magnitude earthquake shook Tagbilaran, Bohol, its force felt throughout the Visayas. It caused more than 120 casualties, and much damage to buildings, historical landmarks and churches. The earthquake destroyed most of the Basilica's belfry and façade; some walls and frescoes were cracked. A video of the collapse can be seen here. The building was soon[when?] restored[citation needed] and later re-opened to the public. The bell tower is now fully reconstructed and the main door of the church as well as the area in between the original church and the pilgrim center is now fully accessible.

The museum was first established in the year 1965 by Fr. Ambrosio Galindez, O.S.A. for the purpose of the commemoration of the Fourth Centennial of the Christianization of the Philippines. It was then located at a certain room in the convent. Old church documents dating back to the 17th century, antique church furniture, antique church things (i.e. Chalice, Altar Table, Thurible, etc.), and antique vestments of the priests are in display. The old vestments of the Sto. Niño de Cebu dating back to the 17th century are also in display. The relics and statues of the different saints are also in exhibit. The replicas of the Sto. Niño used in different pilgrimages in the Philippines and abroad are displayed. Some donated jewelleries and gift toys to the Sto. Niño are in display also.

The Basilica del Sto. Niño Museum is currently located at the basement of the Pilgrim Center.

Originally for exclusive use by the friars, in the year 2000 the church library was opened to all serious nonclerical researchers. Its collection covers religious subjects and non-religious disciplines including history, science, philosophy, Filipiniana, and periodicals.[1]